Laser effects during bleaching

[Martin Spitaler]

Just a note because WinXP-64bit discussions were on here before: Even if the software doesn't support 64 bit, it should run faster because the the 'virtual memory' the software is using (beyond 3GB) is actually stored in RAM rather than on the harddrive.

And thanks for the spoof tip, hopefully it works,

Martin

[Northan, Brian]

Interesting discussion.  First off I am a software engineer at Media Cybernetics, working on the Autoquant product.  

 

Both XCOSM and Autoquant are implementations of the Expectation Maximization algorithm.  In fact they both descend in part from research done by Washington University groups.  Autoquant adds many extensions for acceleration, blind deconvolution, constraints, noise reduction etc.    

 

Given that Autoquant is an extended version of EM, it is designed to outperform a baseline implementation, both in speed and quality of results.   Testing of this has been done over the last 15 years through several SBIRs and research papers.  Still testing is an ongoing process so please let us know about situations where the software could be improved.

 

Keeping in mind that I am an Autoquant developer with an interest in this here are a few suggestions for anybody running tests...

 

1.  Always make all input and output images publicly available so the developers of the software have a chance to run the tests themselves, confirm the results, make sure the software was used properly.

 

2.  Record the scope data (NA, EMW etc.) and deconvolution settings (num. iterations, PSF input etc.) meticulously and make them available.

 

3.  Use the latest version of all products (Autoquant is now at X2.3).

 

4.  If testing speed use a modern PC.  (Much of the latest work in the field is in implementing multi-core and 64 bit versions of the algorithms).

 

5.  Record the effects of Subvoluming: When the image becomes to large to fit into memory it is divided into smaller sub-images, how well an algorithm deals with this is an important consideration.

 

6.  Always output the PSF if the software allows.  Even if you are using fixed PSF deconvolution, the PSF may be manipulated (noise reduction, symmetry constraints).  Much of the difference in algorithm results can be explained by differences in the PSF

 

Anyone doing these tests please keep us updated.

 
All the best
Brian Northan
Software Engineer
Media Cybernetics, Inc.
117E Essex Circle, Guilderland NY
tel [phone]
 

________________________________

From: Confocal Microscopy List on behalf of Stanislav Vitha
Sent: Wed 11/26/2008 2:09 PM
To: [hidden email]
Subject: Re: Deconvolution Algorithms



Some time ago I used XCOSM   http://www.essrl.wustl.edu/~preza/xcosm/
under linux (with graphical user interface), and also in command-line mode on
a Windows machine with cygwin installed.
I did not do any extensive tests, for my few samples I was quite satisfied with
the results. The best algorithm (Expectation Maximization) has very slow
convergence, so you need hundreds or thousands of iterations (= a lot of
time).
I liked the results better than those from the commercial AutoDeblur v. 9.2
package (Blind deconvolution), but on the other hand, there the deconvolution
took about 1/10th of the time.

Sincerely,
Stan Vitha

Microscopy and Imaging Center,
Texas A&M University

:
On Wed, 26 Nov 2008 00:35:13 +0100, Johan Henriksson
<[hidden email]> wrote:

>Neeraj Gohad wrote:
>> Dear List,
>>
>> We are trying to compare open source deconvolution algorithms with the
>> commercial deconvolution package that we have. So far we have tried the
>> Iterative Deconvolve 3D for ImageJ. I wanted to know which other open
>> source algorithms people are using for deconvolution.
>>
>> Best Regards,
>>
>
>haven't tried yet:
>http://piotr.wendykier.googlepages.com/iterativedeconvolution
>
>also used your package there, it failed, and since imagej has problems
>with batching I wouldn't bother with IJ plugins for it anyway. I have
>used my own code in the past, but for special classes of deconv, not the
>normal one in biology. we're writing a new algorithm at the moment.
>
>/Johan
>
>--
>--
>------------------------------------------------
>Johan Henriksson
>MSc Engineering
>PhD student, Karolinska Institutet
>http://mahogny.areta.org <http://mahogny.areta.org/>  http://www.endrov.net <http://www.endrov.net/>

[mahogny]

Martin Spitaler wrote:
> Just a note because WinXP-64bit discussions were on here before: Even
> if the software doesn't support 64 bit, it should run faster because
> the the 'virtual memory' the software is using (beyond 3GB) is
> actually stored in RAM rather than on the harddrive.
this sounds really off to me. virtual memory works by taking a block of
memory and putting it on the harddrive. the address does not change,
there will simply be nothing to where it points. hence virtual memory
*does not* extend your limit past 2gb or 3gb, whatever your OS has.

--
--
------------------------------------------------
Johan Henriksson
MSc Engineering
PhD student, Karolinska Institutet
http://mahogny.areta.org http://www.endrov.net

[Torsten.Fregin]

On 28 Nov 2008 at 18:00, Johan Henriksson wrote:

> Martin Spitaler wrote:
> > Just a note because WinXP-64bit discussions were on here before: Even
> > if the software doesn't support 64 bit, it should run faster because
> > the the 'virtual memory' the software is using (beyond 3GB) is
> > actually stored in RAM rather than on the harddrive.
> this sounds really off to me. virtual memory works by taking a block of
> memory and putting it on the harddrive. the address does not change,
> there will simply be nothing to where it points. hence virtual memory
> *does not* extend your limit past 2gb or 3gb, whatever your OS has.

But how about a RAM-disc?

[mahogny]

[hidden email] wrote:

> On 28 Nov 2008 at 18:00, Johan Henriksson wrote:
>
>  
>> Martin Spitaler wrote:
>>    
>>> Just a note because WinXP-64bit discussions were on here before: Even
>>> if the software doesn't support 64 bit, it should run faster because
>>> the the 'virtual memory' the software is using (beyond 3GB) is
>>> actually stored in RAM rather than on the harddrive.
>>>      
>> this sounds really off to me. virtual memory works by taking a block of
>> memory and putting it on the harddrive. the address does not change,
>> there will simply be nothing to where it points. hence virtual memory
>> *does not* extend your limit past 2gb or 3gb, whatever your OS has.
>>    
>
> But how about a RAM-disc?
>  

a ram disk enables you to use a part of the ram as a harddrive. speeds
up disk I/O, used commonly for /tmp-filesystems on unix, but has nothing
to do with 32-bit addressing limitations.

--
--
------------------------------------------------
Johan Henriksson
MSc Engineering
PhD student, Karolinska Institutet
http://mahogny.areta.org http://www.endrov.net

[Guy Cox]

Yes, if you have 3 GB + memory there will be no paging to
virtual memory (wherever located) in any case.  Virtual
memory is handled by the OS, not the application.   But
swap files on the hard disk (handled by the app) are used
by many imaging programs to let them handle datasets which
exceed addressable space.  With older 8 bit and 16 bit
applications this was common - nowadays I'd have thought a
programme needing more than the 32-bit addressable space
would be written for a 64-bit OS.  But in principle a RAM
disk for the swap files could help speed things up for a
32-bit app on a 64-bit OS.

                                        Guy



Optical Imaging Techniques in Cell Biology
by Guy Cox    CRC Press / Taylor & Francis
    http://www.guycox.com/optical.htm
______________________________________________
Associate Professor Guy Cox, MA, DPhil(Oxon)
Electron Microscope Unit, Madsen Building F09,
University of Sydney, NSW 2006
______________________________________________
Phone [phone]     Fax [phone]
Mobile [phone]
______________________________________________
     http://www.guycox.net
-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Johan Henriksson
Sent: Saturday, 29 November 2008 4:01 AM
To: [hidden email]
Subject: Re: Leica LAF on 64 bit windows?

Martin Spitaler wrote:
> Just a note because WinXP-64bit discussions were on here before: Even
> if the software doesn't support 64 bit, it should run faster because
> the the 'virtual memory' the software is using (beyond 3GB) is
> actually stored in RAM rather than on the harddrive.
this sounds really off to me. virtual memory works by taking a block of memory and putting it on the harddrive. the address does not change, there will simply be nothing to where it points. hence virtual memory *does not* extend your limit past 2gb or 3gb, whatever your OS has.

--
--
------------------------------------------------
Johan Henriksson
MSc Engineering
PhD student, Karolinska Institutet
http://mahogny.areta.org http://www.endrov.net

No virus found in this incoming message.
Checked by AVG.
Version: 7.5.552 / Virus Database: 270.9.11/1818 - Release Date: 28/11/2008 7:31 PM
 

No virus found in this outgoing message.
Checked by AVG.
Version: 7.5.552 / Virus Database: 270.9.11/1818 - Release Date: 28/11/2008 7:31 PM
 

[Page Baluch]

I have a student who would like to use our Leica SP2 confocal to scan small dental casts. Has anyone had experience with this type of technique? It appears that if the teeth are not coated with a fluorescent material and scanned in just a reflective mode there is a lot of artifact that is also captured. She would like to have clean scans to create a 3D rendering so she can compare various casts. There was a previous study that used eosin to coat the cast and they were able to get satisfactory results. Does anyone have suggestions might improve upon this method?

Thanks for your help,
Page

Arizona State University/SoLS
WM Keck Bioimaging Laboratory

[Christian-103]

Page,

I recall many years ago a paper on imaging gorilla teeth using confocal, I believe it was on a Bio-Rad 1024 MRC.  You might put the student on the trail of similar work.

Are you scanning casts of the teeth (a negative or positive cast?) and what scale are we looking at here?  What magnification?

Christian

[jlribas]

Dear Debra,
There are several possibilities to obtain a good surface 3D image of
teeth. Several resins that are routinarily used in dental clinics are
autofluorescents (ask them). Also in EMS there is a silicon gum ready to
use.
The other approach is to cover the surface of the teeth with a saturated
solution of eosin dissolved in acetone and let it drying upside down.
You have to filter the final concentrated solution and use the 543 line
of the HeNe laser. That is, working in fluorescence mode, not in
backscattering.
Another naturally widely distributed molecule for working in this way is
chlorophyll. You can obtain a concentrated solution of chlorophyll
simply introducing some green leaves in acetone and waiting for some
evaporation of the solvent. After several changes, you can obtain a
final saturated solution of chlorophyll (with a bright green color).
Proceed in the same way as eosin but use the 488 line of the argon laser.
Also remember to work with "z-wide" for a bigger z range in the
acquisition mode and configuration of the z button in "z-wide position".

Good luck

Juan Luis


Debra Baluch escribió:
> I have a student who would like to use our Leica SP2 confocal to scan small dental casts. Has anyone had experience with this type of technique? It appears that if the teeth are not coated with a fluorescent material and scanned in just a reflective mode there is a lot of artifact that is also captured. She would like to have clean scans to create a 3D rendering so she can compare various casts. There was a previous study that used eosin to coat the cast and they were able to get satisfactory results. Does anyone have suggestions might improve upon this method?
>
> Thanks for your help,
> Page
>
> Arizona State University/SoLS
> WM Keck Bioimaging Laboratory
>
>  

--
Juan Luis Ribas
Servicio de Microscopía
Centro de Investigación, Tecnología e Innovación
Universidad de Sevilla
Av. Reina Mercedes 4b
41012 Sevilla

Tfno: 954559983

[Stanislav Vitha]

Dear Page,
sorry for the dealy, my previous reply bounced back.

Last year I had a client who wanted imaging of dental casts. In the end, the
fluorescence dye was incorporated in the epoxy resin for the
positive replica (eosin; this was probably based on the the same previous
study that you mention) - but any decent fluorescent dye soluble in non-polar
solvents should work. On some resin casts that were originally not stained I
used Rhodamine B in ethanol, stained in a standard microwave (1000W) for
about 1 min, then rinsed. That also worked fairly well, as long as the dye
solution was filtered before use.
Ideally, the casts should be from an opaque resin, so that the
fluorescent signal is limited to the surface (or stain so intensely so that the
signal drops off fast due to absorption when you get below the surface).
Our goal was to look at micro-wear patterns, rather than at the entire cast,
so we imaged with a 40x/0.6 long working distance objective on our Olympus
confocal, z-step 50 or 100 nm.
 
For processing of the image stacks, I liked best the TopoJ plugin for ImageJ,
generously shared by David Hovis (dbh6 at case.edu). The plugin has been
recently updated with new cool functions and improvements.
The plugin gave much better results that the TOPO projection  function built
in the Olympus confocal software.
Visualization of the topographical  projection was done using ImageJ
plugin "interactive 3D surface Plot v. 2.22"
 
Sincerely,


Stan Vitha


Microscopy and Imaging Center,
Texas A&M University



On Fri, 28 Nov 2008 22:01:25 -0700, Debra Baluch <[hidden email]>
wrote:


>I have a student who would like to use our Leica SP2 confocal to scan small
dental casts. Has anyone had experience with this type of technique? It
appears that if the teeth are not coated with a fluorescent material and
scanned in just a reflective mode there is a lot of artifact that is also
captured. She would like to have clean scans to create a 3D rendering so she
can compare various casts. There was a previous study that used eosin to
coat the cast and they were able to get satisfactory results. Does anyone
have suggestions might improve upon this method?
>
>Thanks for your help,
>Page
>
>Arizona State University/SoLS
>WM Keck Bioimaging Laboratory

[lechristophe]

Dear David,

I'd be interested in a software that makes the LEICA LAS-AF installer think it is installing on a 32-bits Windows XP, because the installer quits under XP 64-bits. Unfortunately, the link below doesn't exist anymore, and I was unable to find such a software by googling...
If David or someone else has a precise reference (linkl/name of the soft) to such a soft, please share !
Thanks a lot,

Christophe Leterrier

On Wed, Nov 26, 2008 at 15:32, David Kelly <[hidden email]> wrote:

Hello Aryeh

It is possible to run LAS on 64bit XP but its not easy. When installing you run the program from the link below. This spoofs LAS into thinking its running on a 32 bit system. The problem is that everytime you upgrade your confocal software you need to upgrade your workstation software and this spoofing doesn't always work. So if you have the time and the inclination you can do it but unless you are dealing with very big image stacks and need the extra memory I wouldn't bother

http://www.microsoft.com/downloads/details.aspx?familyid=bd02c19c-1250-433c-8c1b-2619bd93b3a2&displaylang=en

When this doesn't work there are other utilities that also spoof XP version numbers with varying degrees of success

Hope this helps

Dave

Aryeh Weiss wrote:

I am wondering if anyone on list has run a *second* copy of Leica LAF (not to acquire from the confocal, but an offline copy) on 64 bit Windows? It was my understanding that 32 bit software runs under the 64 bit version, but one never knows.

Thanks in advance.
--aryeh

--

David Kelly
University of Edinburgh
Wellcome Trust Centre for Cell Biology
Michael Swann Building
Mayfield Road
EH9 3JR

Tel: [phone]
E-Mail: [hidden email]
Website: http://www.wcb.ed.ac.uk/COIL


The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

[davek604]

Hello Christophe
If that link is broken try Orca Msi editor, this is a very powerful tool
for editing the windows installer, If you put it into a google search it
should come up in the first couple of hits. I've not used it for LAS-AF
but I have used it for other programs. If I were you I'd give up on LAS
on 32bit or 64bit as its not much good for analysis or viewing. If you
don't want to buy a commercial package I'd go for Image J its miles
ahead of LAS and will work on almost anything.

Cheers

Dave
 
Christophe Leterrier wrote:

> Dear David,
>
> I'd be interested in a software that makes the LEICA LAS-AF installer
> think it is installing on a 32-bits Windows XP, because the installer
> quits under XP 64-bits. Unfortunately, the link below doesn't exist
> anymore, and I was unable to find such a software by googling...
> If David or someone else has a precise reference (linkl/name of the
> soft) to such a soft, please share !
> Thanks a lot,
>
> Christophe Leterrier
>
> On Wed, Nov 26, 2008 at 15:32, David Kelly <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hello Aryeh
>
>     It is possible to run LAS on 64bit XP but its not easy. When
>     installing you run the program from the link below. This spoofs
>     LAS into thinking its running on a 32 bit system. The problem is
>     that everytime you upgrade your confocal software you need to
>     upgrade your workstation software and this spoofing doesn't always
>     work. So if you have the time and the inclination you can do it
>     but unless you are dealing with very big image stacks and need the
>     extra memory I wouldn't bother
>
>     http://www.microsoft.com/downloads/details.aspx?familyid=bd02c19c-1250-433c-8c1b-2619bd93b3a2&displaylang=en
>     <http://www.microsoft.com/downloads/details.aspx?familyid=bd02c19c-1250-433c-8c1b-2619bd93b3a2&displaylang=en>
>
>
>     When this doesn't work there are other utilities that also spoof
>     XP version numbers with varying degrees of success
>
>     Hope this helps
>
>     Dave
>
>
>     Aryeh Weiss wrote:
>
>         I am wondering if anyone on list has run a *second* copy of
>         Leica LAF (not to acquire from the confocal, but an offline
>         copy) on 64 bit Windows? It was my understanding that 32 bit
>         software runs under the 64 bit version, but one never knows.
>
>         Thanks in advance.
>         --aryeh
>
>
>     --
>     David Kelly
>     University of Edinburgh
>     Wellcome Trust Centre for Cell Biology
>     Michael Swann Building
>     Mayfield Road
>     EH9 3JR
>
>     Tel: [phone]
>     E-Mail: [hidden email] <mailto:[hidden email]>
>     Website: http://www.wcb.ed.ac.uk/COIL
>
>
>     The University of Edinburgh is a charitable body, registered in
>     Scotland, with registration number SC005336.
>
>

--
David Kelly
University of Edinburgh
Wellcome Trust Centre for Cell Biology
Michael Swann Building
Mayfield Road
EH9 3JR

Tel: [phone]
E-Mail: [hidden email]
Website: http://coil.bio.ed.ac.uk/


The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

[lechristophe]

David,

The leica LAS-AF Lite is not a msi file, it is an exe that (temporarily) extract a msi but I could'nt access it before it is being deleted by the installer (as soon as it detects that it is running under 64b XP), so an msi editor is not usable I guess. I tried to execute the exe in XP compatibility mode but without luck. Trying all available versions of LAS AF Lite, the 2.0.0 (build 1934) could install without checking compatibility (I guess it is a bug, since 2.0.2 refuses to install), but launching LAS after install was not possible, here is the error for those who are interested :

System.BadImageFormatException: Could not load file or assembly 'LMSDataContainerWrapper, Version=1.6.1365.1, Culture=neutral, PublicKeyToken=649f33ec29f0c41f' or one of its dependencies. An attempt was made to load a program with an incorrect format.
File name: 'LMSDataContainerWrapper, Version=1.6.1365.1, Culture=neutral, PublicKeyToken=649f33ec29f0c41f'
   at LASLife.DataManager.SetLogFileName(String LogFileName)
   at LASAFApplication.MainEntryPoint.MainSTAInner(String[] args, Boolean bLite, String LogFilePath)
   at LASAFApplication.MainEntryPoint.MainSTA2()

By the way, I'm very well aware of the limitations of LAS software, I use ImageJ primarily but I wanted to have LAS-AF Lite installed on an offline analysis computer in order for the users to be able to edit their experiment .LIF files (such as changing names, check image scales and metadata, reorganizing images in experiments), as ImageJ/BioFormats does not allow to seamlessly open and save .LIF files. BioFormats handles .LIF quite well (I contributed files and bug reports) but I always prefer to check metadata in the primary software in case of doubt.

Thanks a lot for your help,

Christophe Leterrier

On Tue, Mar 10, 2009 at 11:23, David Kelly <[hidden email]> wrote:

Hello Christophe
If that link is broken try Orca Msi editor, this is a very powerful tool for editing the windows installer, If you put it into a google search it should come up in the first couple of hits. I've not used it for LAS-AF but I have used it for other programs. If I were you I'd give up on LAS on 32bit or 64bit as its not much good for analysis or viewing. If you don't want to buy a commercial package I'd go for Image J its miles ahead of LAS and will work on almost anything.

Cheers

Dave

Christophe Leterrier wrote:

Dear David,

I'd be interested in a software that makes the LEICA LAS-AF installer think it is installing on a 32-bits Windows XP, because the installer quits under XP 64-bits. Unfortunately, the link below doesn't exist anymore, and I was unable to find such a software by googling...
If David or someone else has a precise reference (linkl/name of the soft) to such a soft, please share !
Thanks a lot,

Christophe Leterrier

On Wed, Nov 26, 2008 at 15:32, David Kelly <[hidden email] <mailto:[hidden email]>> wrote:

   Hello Aryeh

   It is possible to run LAS on 64bit XP but its not easy. When
   installing you run the program from the link below. This spoofs
   LAS into thinking its running on a 32 bit system. The problem is
   that everytime you upgrade your confocal software you need to
   upgrade your workstation software and this spoofing doesn't always
   work. So if you have the time and the inclination you can do it
   but unless you are dealing with very big image stacks and need the
   extra memory I wouldn't bother

   http://www.microsoft.com/downloads/details.aspx?familyid=bd02c19c-1250-433c-8c1b-2619bd93b3a2&displaylang=en
   <http://www.microsoft.com/downloads/details.aspx?familyid=bd02c19c-1250-433c-8c1b-2619bd93b3a2&displaylang=en>


   When this doesn't work there are other utilities that also spoof
   XP version numbers with varying degrees of success

   Hope this helps

   Dave


   Aryeh Weiss wrote:

       I am wondering if anyone on list has run a *second* copy of
       Leica LAF (not to acquire from the confocal, but an offline
       copy) on 64 bit Windows? It was my understanding that 32 bit
       software runs under the 64 bit version, but one never knows.

       Thanks in advance.
       --aryeh


   --    David Kelly
   University of Edinburgh
   Wellcome Trust Centre for Cell Biology
   Michael Swann Building
   Mayfield Road
   EH9 3JR

   Tel: [phone]

   E-Mail: [hidden email] <mailto:[hidden email]>

   Website: http://www.wcb.ed.ac.uk/COIL


   The University of Edinburgh is a charitable body, registered in
   Scotland, with registration number SC005336.

--
David Kelly
University of Edinburgh
Wellcome Trust Centre for Cell Biology
Michael Swann Building
Mayfield Road
EH9 3JR

Tel: [phone]
E-Mail: [hidden email]

Website: http://coil.bio.ed.ac.uk/

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

[davek604]

Hello Christophe

As far as i can make out that error is terminal for your chances of
running it in 64bit.  It looks like the .dll file for the data container
hasn't been compiled in 32bit mode which means the OS attempts to run it
in 64bit mode rather than 32bit and can't. All it requires is for Leica
to compile this .dll  for 32bit mode only and it will work, they don't
even need to rewrite it for 64 bit. So Leica I know your watching,
please sort it out

Cheers

Dave

Christophe Leterrier wrote:

> David,
>
> The leica LAS-AF Lite is not a msi file, it is an exe that
> (temporarily) extract a msi but I could'nt access it before it is
> being deleted by the installer (as soon as it detects that it is
> running under 64b XP), so an msi editor is not usable I guess. I tried
> to execute the exe in XP compatibility mode but without luck. Trying
> all available versions of LAS AF Lite, the 2.0.0 (build 1934) could
> install without checking compatibility (I guess it is a bug, since
> 2.0.2 refuses to install), but launching LAS after install was not
> possible, here is the error for those who are interested :
>
> System.BadImageFormatException: Could not load file or assembly
> 'LMSDataContainerWrapper, Version=1.6.1365.1, Culture=neutral,
> PublicKeyToken=649f33ec29f0c41f' or one of its dependencies. An
> attempt was made to load a program with an incorrect format.
> File name: 'LMSDataContainerWrapper, Version=1.6.1365.1,
> Culture=neutral, PublicKeyToken=649f33ec29f0c41f'
>    at LASLife.DataManager.SetLogFileName(String LogFileName)
>    at LASAFApplication.MainEntryPoint.MainSTAInner(String[] args,
> Boolean bLite, String LogFilePath)
>    at LASAFApplication.MainEntryPoint.MainSTA2()
>
> By the way, I'm very well aware of the limitations of LAS software, I
> use ImageJ primarily but I wanted to have LAS-AF Lite installed on an
> offline analysis computer in order for the users to be able to edit
> their experiment .LIF files (such as changing names, check image
> scales and metadata, reorganizing images in experiments), as
> ImageJ/BioFormats does not allow to seamlessly open and save .LIF
> files. BioFormats handles .LIF quite well (I contributed files and bug
> reports) but I always prefer to check metadata in the primary software
> in case of doubt.
>
> Thanks a lot for your help,
>
> Christophe Leterrier
>
>
>
> On Tue, Mar 10, 2009 at 11:23, David Kelly <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hello Christophe
>     If that link is broken try Orca Msi editor, this is a very
>     powerful tool for editing the windows installer, If you put it
>     into a google search it should come up in the first couple of
>     hits. I've not used it for LAS-AF but I have used it for other
>     programs. If I were you I'd give up on LAS on 32bit or 64bit as
>     its not much good for analysis or viewing. If you don't want to
>     buy a commercial package I'd go for Image J its miles ahead of LAS
>     and will work on almost anything.
>
>     Cheers
>
>     Dave
>
>     Christophe Leterrier wrote:
>
>         Dear David,
>
>         I'd be interested in a software that makes the LEICA LAS-AF
>         installer think it is installing on a 32-bits Windows XP,
>         because the installer quits under XP 64-bits. Unfortunately,
>         the link below doesn't exist anymore, and I was unable to find
>         such a software by googling...
>         If David or someone else has a precise reference (linkl/name
>         of the soft) to such a soft, please share !
>         Thanks a lot,
>
>         Christophe Leterrier
>
>         On Wed, Nov 26, 2008 at 15:32, David Kelly
>         <[hidden email]
>         <mailto:[hidden email]>
>         <mailto:[hidden email]
>         <mailto:[hidden email]>>> wrote:
>
>            Hello Aryeh
>
>            It is possible to run LAS on 64bit XP but its not easy. When
>            installing you run the program from the link below. This spoofs
>            LAS into thinking its running on a 32 bit system. The
>         problem is
>            that everytime you upgrade your confocal software you need to
>            upgrade your workstation software and this spoofing doesn't
>         always
>            work. So if you have the time and the inclination you can do it
>            but unless you are dealing with very big image stacks and
>         need the
>            extra memory I wouldn't bother
>
>          
>          http://www.microsoft.com/downloads/details.aspx?familyid=bd02c19c-1250-433c-8c1b-2619bd93b3a2&displaylang=en
>         <http://www.microsoft.com/downloads/details.aspx?familyid=bd02c19c-1250-433c-8c1b-2619bd93b3a2&displaylang=en>
>          
>          <http://www.microsoft.com/downloads/details.aspx?familyid=bd02c19c-1250-433c-8c1b-2619bd93b3a2&displaylang=en
>         <http://www.microsoft.com/downloads/details.aspx?familyid=bd02c19c-1250-433c-8c1b-2619bd93b3a2&displaylang=en>>
>
>
>            When this doesn't work there are other utilities that also
>         spoof
>            XP version numbers with varying degrees of success
>
>            Hope this helps
>
>            Dave
>
>
>            Aryeh Weiss wrote:
>
>                I am wondering if anyone on list has run a *second* copy of
>                Leica LAF (not to acquire from the confocal, but an offline
>                copy) on 64 bit Windows? It was my understanding that
>         32 bit
>                software runs under the 64 bit version, but one never
>         knows.
>
>                Thanks in advance.
>                --aryeh
>
>
>            --    David Kelly
>            University of Edinburgh
>            Wellcome Trust Centre for Cell Biology
>            Michael Swann Building
>            Mayfield Road
>            EH9 3JR
>
>            Tel: [phone]
>            E-Mail: [hidden email]
>         <mailto:[hidden email]>
>         <mailto:[hidden email]
>         <mailto:[hidden email]>>
>
>            Website: http://www.wcb.ed.ac.uk/COIL
>
>
>            The University of Edinburgh is a charitable body, registered in
>            Scotland, with registration number SC005336.
>
>
>
>     --
>     David Kelly
>     University of Edinburgh
>     Wellcome Trust Centre for Cell Biology
>     Michael Swann Building
>     Mayfield Road
>     EH9 3JR
>
>     Tel: [phone]
>     E-Mail: [hidden email] <mailto:[hidden email]>
>     Website: http://coil.bio.ed.ac.uk/
>
>
>
>     The University of Edinburgh is a charitable body, registered in
>     Scotland, with registration number SC005336.
>
>

--
David Kelly
University of Edinburgh
Wellcome Trust Centre for Cell Biology
Michael Swann Building
Mayfield Road
EH9 3JR

Tel: [phone]
E-Mail: [hidden email]
Website: http://coil.bio.ed.ac.uk/


The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

[David Strachan]

Hi Christophe,

This does not solve your problems but you stated the following ...
> The leica LAS-AF Lite is not a msi file, it is an exe that
> (temporarily) extract a msi but I could'nt access it before it is
> being deleted by the installer

The LASAF Lite exe is a self extracting zip file which can be opened
with utilities such as WINRAR, shareware (Since WINRAR does all I need I
have not got ZIP installed so cannot say for definite but I suspect that
this will also open it)

You can extract the files contained in the exe to a folder to reveal the
following that are inside

16/12/2008  13:26                27 AUTORUN.inf
16/12/2008  14:03        26,694,686 data1.cab
16/12/2008  14:03            22,590 data1.hdr
16/12/2008  14:03        30,199,851 data2.cab
12/03/2009  11:10                 0 directory.txt
18/04/2007  19:06           535,552 ISSetup.dll
16/12/2008  14:03               475 layout.bin
16/12/2008  14:03           372,736 setup.exe
16/12/2008  14:03               495 setup.ini
16/12/2008  14:03           244,412 setup.inx
24/04/2007  17:21           156,616 _Setup.dll
             
There is setup.exe that actually does the install. So whatever software
you use to spoof your OS to this file may work allowing you to install.
Whether it will run properly is another thing of course.

Hope this helps you get another step towards the goal.



David Strachan

Beatson Advanced Imaging Resource (BAIR)
The Beatson Institute for Cancer Research
Garscube Estate, Switchback Road, Glasgow  G61 1BD
 
 
( Direct Line [phone]
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transmission in error please would you be kind enough to inform us.
-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]]
On Behalf Of David Kelly
Sent: 10 March 2009 14:46
To: [hidden email]
Subject: Re: Leica LAF on 64 bit windows?

Hello Christophe

As far as i can make out that error is terminal for your chances of
running it in 64bit.  It looks like the .dll file for the data container

hasn't been compiled in 32bit mode which means the OS attempts to run it

in 64bit mode rather than 32bit and can't. All it requires is for Leica
to compile this .dll  for 32bit mode only and it will work, they don't
even need to rewrite it for 64 bit. So Leica I know your watching,
please sort it out

Cheers

Dave

Christophe Leterrier wrote:
> David,
>
> The leica LAS-AF Lite is not a msi file, it is an exe that
> (temporarily) extract a msi but I could'nt access it before it is
> being deleted by the installer (as soon as it detects that it is
> running under 64b XP), so an msi editor is not usable I guess. I tried

> to execute the exe in XP compatibility mode but without luck. Trying
> all available versions of LAS AF Lite, the 2.0.0 (build 1934) could
> install without checking compatibility (I guess it is a bug, since
> 2.0.2 refuses to install), but launching LAS after install was not
> possible, here is the error for those who are interested :
>
> System.BadImageFormatException: Could not load file or assembly
> 'LMSDataContainerWrapper, Version=1.6.1365.1, Culture=neutral,
> PublicKeyToken=649f33ec29f0c41f' or one of its dependencies. An
> attempt was made to load a program with an incorrect format.
> File name: 'LMSDataContainerWrapper, Version=1.6.1365.1,
> Culture=neutral, PublicKeyToken=649f33ec29f0c41f'
>    at LASLife.DataManager.SetLogFileName(String LogFileName)
>    at LASAFApplication.MainEntryPoint.MainSTAInner(String[] args,
> Boolean bLite, String LogFilePath)
>    at LASAFApplication.MainEntryPoint.MainSTA2()
>
> By the way, I'm very well aware of the limitations of LAS software, I
> use ImageJ primarily but I wanted to have LAS-AF Lite installed on an
> offline analysis computer in order for the users to be able to edit
> their experiment .LIF files (such as changing names, check image
> scales and metadata, reorganizing images in experiments), as
> ImageJ/BioFormats does not allow to seamlessly open and save .LIF
> files. BioFormats handles .LIF quite well (I contributed files and bug

> reports) but I always prefer to check metadata in the primary software

> in case of doubt.
>
> Thanks a lot for your help,
>
> Christophe Leterrier
>
>
>
> On Tue, Mar 10, 2009 at 11:23, David Kelly <[hidden email]

> <mailto:[hidden email]>> wrote:
>
>     Hello Christophe
>     If that link is broken try Orca Msi editor, this is a very
>     powerful tool for editing the windows installer, If you put it
>     into a google search it should come up in the first couple of
>     hits. I've not used it for LAS-AF but I have used it for other
>     programs. If I were you I'd give up on LAS on 32bit or 64bit as
>     its not much good for analysis or viewing. If you don't want to
>     buy a commercial package I'd go for Image J its miles ahead of LAS
>     and will work on almost anything.
>
>     Cheers
>
>     Dave
>
>     Christophe Leterrier wrote:
>
>         Dear David,
>
>         I'd be interested in a software that makes the LEICA LAS-AF
>         installer think it is installing on a 32-bits Windows XP,
>         because the installer quits under XP 64-bits. Unfortunately,
>         the link below doesn't exist anymore, and I was unable to find
>         such a software by googling...
>         If David or someone else has a precise reference (linkl/name
>         of the soft) to such a soft, please share !
>         Thanks a lot,
>
>         Christophe Leterrier
>
>         On Wed, Nov 26, 2008 at 15:32, David Kelly
>         <[hidden email]
>         <mailto:[hidden email]>
>         <mailto:[hidden email]
>         <mailto:[hidden email]>>> wrote:
>
>            Hello Aryeh
>
>            It is possible to run LAS on 64bit XP but its not easy.

When
>            installing you run the program from the link below. This
spoofs
>            LAS into thinking its running on a 32 bit system. The
>         problem is
>            that everytime you upgrade your confocal software you need
to
>            upgrade your workstation software and this spoofing doesn't
>         always
>            work. So if you have the time and the inclination you can
do it
>            but unless you are dealing with very big image stacks and
>         need the
>            extra memory I wouldn't bother
>
>          
>
http://www.microsoft.com/downloads/details.aspx?familyid=bd02c19c-1250-4
33c-8c1b-2619bd93b3a2&displaylang=en
>
<http://www.microsoft.com/downloads/details.aspx?familyid=bd02c19c-1250-
433c-8c1b-2619bd93b3a2&displaylang=en>
>          
>
<http://www.microsoft.com/downloads/details.aspx?familyid=bd02c19c-1250-
433c-8c1b-2619bd93b3a2&displaylang=en
>
<http://www.microsoft.com/downloads/details.aspx?familyid=bd02c19c-1250-
433c-8c1b-2619bd93b3a2&displaylang=en>>

>
>
>            When this doesn't work there are other utilities that also
>         spoof
>            XP version numbers with varying degrees of success
>
>            Hope this helps
>
>            Dave
>
>
>            Aryeh Weiss wrote:
>
>                I am wondering if anyone on list has run a *second*

copy of
>                Leica LAF (not to acquire from the confocal, but an
offline

>                copy) on 64 bit Windows? It was my understanding that
>         32 bit
>                software runs under the 64 bit version, but one never
>         knows.
>
>                Thanks in advance.
>                --aryeh
>
>
>            --    David Kelly
>            University of Edinburgh
>            Wellcome Trust Centre for Cell Biology
>            Michael Swann Building
>            Mayfield Road
>            EH9 3JR
>
>            Tel: [phone]
>            E-Mail: [hidden email]
>         <mailto:[hidden email]>
>         <mailto:[hidden email]
>         <mailto:[hidden email]>>
>
>            Website: http://www.wcb.ed.ac.uk/COIL
>
>
>            The University of Edinburgh is a charitable body,

registered in

>            Scotland, with registration number SC005336.
>
>
>
>     --
>     David Kelly
>     University of Edinburgh
>     Wellcome Trust Centre for Cell Biology
>     Michael Swann Building
>     Mayfield Road
>     EH9 3JR
>
>     Tel: [phone]
>     E-Mail: [hidden email]

<mailto:[hidden email]>
>     Website: http://coil.bio.ed.ac.uk/
>
>
>
>     The University of Edinburgh is a charitable body, registered in
>     Scotland, with registration number SC005336.
>
>

--
David Kelly
University of Edinburgh
Wellcome Trust Centre for Cell Biology
Michael Swann Building
Mayfield Road
EH9 3JR

Tel: [phone]
E-Mail: [hidden email]
Website: http://coil.bio.ed.ac.uk/


The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.